Bacteriorhodopsin (bR ) is a membrane protein that functions as alight-driven proton pump in the cell membrane of Halobacteriumhalobium. The function is achieved through a cyclic process initiated by the absorption of a photon.The pump cycle is characterized through a series of intermediates J625, K590, L550, M412,N520, and O640, where the subscripts denote the wavelengths ofthe respective absorption maxima [53]. Molecular dynamics simulations have been carried out to studythe J625and K590 intermediates of bR , starting from a refined structure of bR568. The coupling between the electronic states ofretinal and the protein matrix is characterized by the energy difference between the excited state and the ground state to whichthe protein contributes through the Coulomb interaction.Oursimulations indicate that the J625intermediate is related to a polarization of the protein matrix due to the brief (200 fs) changeof retinal's charge distribution in going to the excited state and back to the ground state, and that the rise time of the K590 intermediate is determined by vibrational cooling of retinal. Molecular dynamics simulations of wild-type bR and of its D85N,D85T, D212N, and Y57F mutants have also been carried out to investigate possible differences in the photoproducts of these proteins. For each mutant, a series of 50 molecular dynamics simulations of the photoisomerization and subsequent relaxation process were completed, employing the method in [29]. The 13-cispho-toproducts can be classified into two distinct classes:(1) with the retinal NH+ bond oriented toward Asp-96; (2) with the retinal NH+ bond oriented toward Asp-85 and hydrogen-bonded to a water molecule. Simulations of wild-type bR and of its Y57F mutant resulted mainly in class 1 and class 2 products; simulationsof D85N, D85T, and D212N mutants resulted almost entirely inclass 1 products. These results support the suggestion that only class 2 products initiate a functional pump cycle.